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- PDB-2p7o: Crystal structure of genomically encoded fosfomycin resistance pr... -

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Basic information

Entry
Database: PDB / ID: 2p7o
TitleCrystal structure of genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes (tetragonal form)
ComponentsGlyoxalase family protein
KeywordsMETAL BINDING PROTEIN / hydrolase / FOSFOMYCIN RESISTANCE PROTEIN / MN BINDING / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


response to antibiotic / metal ion binding / cytoplasm
Similarity search - Function
Fosfomycin resistance protein FosX / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / : / Fosfomycin resistance protein FosX
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsFillgrove, K.L. / Pakhomova, S. / Schaab, M. / Newcomer, M.E. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and Mechanism of the Genomically Encoded Fosfomycin Resistance Protein, FosX, from Listeria monocytogenes.
Authors: Fillgrove, K.L. / Pakhomova, S. / Schaab, M.R. / Newcomer, M.E. / Armstrong, R.N.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase family protein
B: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2914
Polymers31,1812
Non-polymers1102
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-39 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.579, 68.579, 56.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Glyoxalase family protein


Mass: 15590.603 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q71YW5, UniProt: Q8Y6I2*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 22% PEG 3350, 0.1 M Tris-HCl, 0.2 M MgCl2, 5% isopropanol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 14, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.44→30 Å / Num. all: 41281 / Num. obs: 41281 / % possible obs: 86.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.048 / Net I/σ(I): 24.4
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2325 / Rsym value: 0.478 / % possible all: 97.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P7K

2p7k


Resolution: 1.44→10 Å / Num. parameters: 20274 / Num. restraintsaints: 25273 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1453 3.8 %RANDOM
Rwork0.124 ---
all0.126 38298 --
obs0.126 38298 80.5 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2223
Refinement stepCycle: LAST / Resolution: 1.44→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 2 168 2220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0342
X-RAY DIFFRACTIONs_zero_chiral_vol0.133
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.156
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0.075

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